Error of java path on loading rJava package

Question

I am trying to load 'rJava' package in my Unix machine. Before loading I have set the path using

Sys.setenv("JAVA_HOME= myfilepath") 

in my R script.

Despite this I am getting the following error (Below is the part of the error):

checking Java support in R... present:
interpreter : '/usr/lib/jvm/jre/bin/java'
archiver    : '/usr/lib/jvm/jre/../bin/jar'
compiler    : '/usr/lib/jvm/jre/../bin/javac'
header prep.: '/usr/lib/jvm/jre/../bin/javah'
cpp flags   : '-I/usr/lib/jvm/java/include I/usr/lib/jvm/java/include/linux'
java libs   : '-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server -ljvm'
checking whether Java run-time works... ./configure: line 3729: /usr/lib/jvm/jre/bin/java: No such file or directory
no configure: error: Java interpreter '/usr/lib/jvm/jre/bin/java' does not work

As you can see the error shows that /usr/lib/jvm/jre/bin/java: No such file or directory. But I have not set this as myfilepath. How do I prevent the installer from looking at this path?

Kindly help.

Solution 1

sudo R CMD javareconf

This works perfectly. Keeping this here if someone reads this in future.

Solution 2

I have a VM of Ubuntu 14.04 LTS on VirtualBox, and the real path of installation of my java-jdk is the following :

/usr/lib/jvm/java-7-openjdk-amd64

This command worked very fine for my situation. I had this type of error from installation o rJava package on RStudio:

*./configure: line 3736: /usr/lib/jvm/default-java/jre/bin/java: No such file or directory*

First I' have modified the profile in this way : sudo gedit /etc/profile and then added this instructions at the eof:

JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64
PATH=$PATH:$HOME/bin:$JAVA_HOME/bin
export JAVA_HOME
export PATH

After this, from terminal session I've typed the command:

sudo R CMD javareconf

and the package rJava was successfully installed.

Note: You might also have to set the LD_LIBRARY_PATH environment variable, before running sudo R CMD javareconf.

Comments

[David Arenburg]

Take a look here maybe. There are some good tips there.

[Aman Mathur]

I had check that post before posting the question. I tried everything there. Does not seem to work for me.

[Manoj G]

Did you tried sudo R CMD javareconf I had the same problem. rJava trying to check the directories which is not at all there in my system. But after running the above config command, it worked for me.

[gladmax]

thanks Manoj sudo R CMD javareconf worked for me.

[CoderGuy123]

This didn't have any effect for me (Mint 18).

[pableiros]

Links to external resources are encouraged, but please add context around the link so your fellow users will have some idea what it is and why it’s there. Always quote the most relevant part of an important link, in case the target site is unreachable or goes permanently offline.

[ZN13]

@Deleet Worked for me (Ubuntu Server 16.04) , after I installed openjdk-7-jdk

[quintindk]

Worked for me, ubuntu 16.04.2!

[joaoal]

For this to work you need to have java installed first. See here for instructions: stackoverflow.com/questions/14788345/…

[Leo]

After sudo R CMD javareconf, run sudo rstudio-server restart.

[2D1C]

Also note that as of version 0.9-12(2020-03-23) rJava has an --enable-dynload option to enable dynamic loading of the JVM. The changelog also shows the order rJava uses to search for the JVM which might be useful. github.com/s-u/rJava/blob/master/NEWS